VS2 issue

[drob2727]

ViWrap run --input_metagenome /home/fslcollab273/nobackup/archive/SALSA_Assembly/SALSA_ASSEMBLY/final_assembly.fasta \ --input_reads /home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_1.fastq,/home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_2.fastq \ --out_dir ./ViWrapTest_DR \ --db_dir /home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap_db \ --identify_method vs \ --conda_env_dir /home/fslcollab273/.conda/envs \ --threads 128 \ --virome \ --input_length_limit 5000

Welcome to ViWrap

The issued command is: /home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap-1.3.0/ViWrap run --input_metagenome /home/fslcollab273/nobackup/archive/SALSA_Assembly/SALSA_ASSEMBLY/final_assembly.fasta --input_reads /home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_1.fastq,/home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_2.fastq --out_dir ./ViWrapTest_DR --db_dir /home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap_db --identify_method vs --conda_env_dir /home/fslcollab273/.conda/envs --threads 128 --virome --input_length_limit 5000

[2024-09-19 20:03:39] | Pre-check inputings. In processing... [2024-09-19 20:08:40] | Looks like the input metagenome and reads, database, and custom MAGs dir (if option used) are now set up well, start up to run ViWrap pipeline [2024-09-19 20:08:40] | Run VirSorter2 to identify viruses from input metagenome. Also plus CheckV to QC and trim, and KEGG, Pfam, and VOG HMMs to annotate viruses. In processing... [2024-09-19 20:09:39] | Run VirSorter2 to identify viruses from input metagenome. Finished [2024-09-19 20:09:41] | Run CheckV to QC and trim viruses identified from VirSorter2. Finished Traceback (most recent call last): File "/home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap-1.3.0/ViWrap", line 173, in output = cli() File "/home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap-1.3.0/ViWrap", line 167, in cli args"func" File "/nobackup/archive/grp/grp_metawrap/ViWrap_DR/ViWrap-1.3.0/scripts/master_run.py", line 179, in main scripts.module.screen_virsorter2_result(args['virsorter_outdir'], keep1_list_file, keep2_list_file, discard_list_file, manual_check_list_file) File "/nobackup/archive/grp/grp_metawrap/ViWrap_DR/ViWrap-1.3.0/scripts/module.py", line 2096, in screen_virsorter2_result with open(final_viral_score, 'r') as lines: FileNotFoundError: [Errno 2] No such file or directory: './ViWrapTest_DR/00_VirSorter_final_assembly/pass/final-viral-score.tsv'

[Drob84761]

Why would VS2 be running through the assembly in 1 minute? I installed everything according to the instructions and had no issues but running the software is not working. I have previously ran VS2 on this assembly and got 1200 viromes over 5000 bp. I used this one to test because my other dataset was getting the same issue. I am running this on a sbatch script if that helps.

[yyyangzd]

Did you solve the problem? I have the same problem too.

[Drob84761]

No I haven't yet. Ive been working on it for days. I think the issue is with the master set up script. My conda environments are so much smaller than what they are supposed to be. I have ran the set-up with every variation I can think of. Im out of ideas.

[try-hunter]

You can check if there is a yaml file and the corresponding conda environment in the conda_env file under the vs section in your database. This issue troubled me for a long time, until I discovered that the size of my database download was incorrect, and the conda environment was missing.